MsmK is thought to import raffinose, and RafEFG is also thought to import raffinose, and d-galactose, melibiose, and stachyose.

There is no experimental evidence that I know of suggesting that MsmK and RafEFG form a transporter complex together.

Both models MsmRaf and MsmRaf2G are modelled with 2R6G as a template.
The difference between them is that MsmRaf chain F is modelled on 2R6G chain F,
whereas MsmRaf2G chain F is modelled on 2R6G chain G. In both models MsmRaf chain G is modelled on 2R6G chain G.
Energy calculations show that MsmRaf chain F seems to be better modelled by 2R6G chain G and by 2R6G chain F.

PDB file of this 3D homology modelPDB file of this 3D homology model with secondary structure assigned by STRIDE
(with incomplete formatting and information)PDB file of this 3D homology model with some residues removed
(those residues that protrude from the template were removed for docking purposes)PDB file of PDBID 2R6G which was used as a template for this 3D homology model

Energy plots of template and homology models from Modeller of NP_346328 (Raf chain E) modelled on 2R6G chain E.
The 1st model (red) was chosen as the final model.

Valpred3D/Profiles3D/REPIMPS plots of final homology model from Modeller of NP_346328 (Raf chain E) modelled on 2R6G chain E.
Solvent accessible surface area (SASA) calculations done on the chain in isolation, not in the complex with other subunits.

Energy plots of template and homology models from Modeller of NP_346327 (Raf chain F) modelled on 2R6G chain G.
The 1st model (red) was chosen as the final model.

Valpred3D/Profiles3D/REPIMPS plots of final homology model from Modeller of NP_346327 (Raf chain F) modelled on 2R6G chain G.
Solvent accessible surface area (SASA) calculations done on the chain in isolation, not in the complex with other subunits.

Energy plots of template and homology models from Modeller of NP_346326 (Raf chain G) modelled on 2R6G chain G.
The 1st model (red) was chosen as the final model.

Valpred3D/Profiles3D/REPIMPS plots of final homology model from Modeller of NP_346326 (Raf chain G) modelled on 2R6G chain G.
Solvent accessible surface area (SASA) calculations done on the chain in isolation, not in the complex with other subunits.

Energy plots of template and homology models from Modeller of NP_346026 (MsmK) modelled on 2R6G chain A.
The 1st model (red) was chosen as the final model.

Valpred3D/Profiles3D/REPIMPS plots of final homology model from Modeller of NP_346026 (MsmK) modelled on 2R6G chain A.
Solvent accessible surface area (SASA) calculations done on the chain in isolation, not in the complex with other subunits.

Energy plots of template and homology models from Modeller of NP_346026 (MsmK) modelled on 2R6G chain B.
The 1st model (red) was chosen as the final model.

Valpred3D/Profiles3D/REPIMPS plots of final homology model from Modeller of NP_346026 (MsmK) modelled on 2R6G chain B.
Solvent accessible surface area (SASA) calculations done on the chain in isolation, not in the complex with other subunits.

MsmK is thought to import raffinose, and RafEFG is also thought to import raffinose, and d-galactose, melibiose, and stachyose.

There is no experimental evidence that I know of suggesting that MsmK and RafEFG form a transporter complex together.

Both models MsmRaf and MsmRaf2G are modelled with 2R6G as a template.
The difference between them is that MsmRaf chain F is modelled on 2R6G chain F,
whereas MsmRaf2G chain F is modelled on 2R6G chain G. In both models MsmRaf chain G is modelled on 2R6G chain G.
Energy calculations show that MsmRaf chain F seems to be better modelled by 2R6G chain G and by 2R6G chain F.

PDB file of this 3D homology modelPDB file of this 3D homology model with secondary structure assigned by STRIDE
(with incomplete formatting and information)PDB file of this 3D homology model with some residues removed
(those residues that protrude from the template were removed for docking purposes)PDB file of PDBID 2R6G which was used as a template for this 3D homology model

Energy plots of template and homology models from Modeller of NP_346328 (Raf chain E) modelled on 2R6G chain E.
The 1st model (red) was chosen as the final model.

Valpred3D/Profiles3D/REPIMPS plots of final homology model from Modeller of NP_346328 (Raf chain E) modelled on 2R6G chain E.
Solvent accessible surface area (SASA) calculations done on the chain in isolation, not in the complex with other subunits.

Valpred3D/Profiles3D/REPIMPS plots of final homology model from Modeller of NP_346328 (Raf chain E) modelled on 2R6G chain E.
Solvent accessible surface area (SASA) calculations done on the chain in the complex with other subunits, not in isolation.

Energy plots of template and homology models from Modeller of NP_346327 (Raf chain F) modelled on 2R6G chain F.
The 1st model (red) was chosen as the final model.

Valpred3D/Profiles3D/REPIMPS plots of final homology model from Modeller of NP_346327 (Raf chain F) modelled on 2R6G chain F.
Solvent accessible surface area (SASA) calculations done on the chain in isolation, not in the complex with other subunits.

Valpred3D/Profiles3D/REPIMPS plots of final homology model from Modeller of NP_346327 (Raf chain F) modelled on 2R6G chain F.
Solvent accessible surface area (SASA) calculations done on the chain in the complex with other subunits, not in isolation.

Energy plots of template and homology models from Modeller of NP_346326 (Raf chain G) modelled on 2R6G chain G.
The 1st model (red) was chosen as the final model.

Valpred3D/Profiles3D/REPIMPS plots of final homology model from Modeller of NP_346326 (Raf chain G) modelled on 2R6G chain G.
Solvent accessible surface area (SASA) calculations done on the chain in isolation, not in the complex with other subunits.

Valpred3D/Profiles3D/REPIMPS plots of final homology model from Modeller of NP_346326 (Raf chain G) modelled on 2R6G chain G.
Solvent accessible surface area (SASA) calculations done on the chain in the complex with other subunits, not in isolation.

Energy plots of template and homology models from Modeller of NP_346026 (MsmK) modelled on 2R6G chain A.
The 1st model (red) was chosen as the final model.

Valpred3D/Profiles3D/REPIMPS plots of final homology model from Modeller of NP_346026 (MsmK) modelled on 2R6G chain A.
Solvent accessible surface area (SASA) calculations done on the chain in isolation, not in the complex with other subunits.

Valpred3D/Profiles3D/REPIMPS plots of final homology model from Modeller of NP_346026 (MsmK) modelled on 2R6G chain A.
Solvent accessible surface area (SASA) calculations done on the chain in the complex with other subunits, not in isolation.

Energy plots of template and homology models from Modeller of NP_346026 (MsmK) modelled on 2R6G chain B.
The 1st model (red) was chosen as the final model.

Valpred3D/Profiles3D/REPIMPS plots of final homology model from Modeller of NP_346026 (MsmK) modelled on 2R6G chain B.
Solvent accessible surface area (SASA) calculations done on the chain in isolation, not in the complex with other subunits.

Valpred3D/Profiles3D/REPIMPS plots of final homology model from Modeller of NP_346026 (MsmK) modelled on 2R6G chain B.
Solvent accessible surface area (SASA) calculations done on the chain in the complex with other subunits, not in isolation.

MsmK is thought to import raffinose, and RafEFG is also thought to import raffinose, and d-galactose, melibiose, and stachyose.

There is no experimental evidence that I know of suggesting that MsmK and RafEFG form a transporter complex together.
This 3D homology model has built them together as a complex due to the following clues :

Here is an operon that might contain the rest of the pieces to the MsmK gene.
MsmK is the ABC-binding part of a raffinose/d-galactose/melibiose/stachyose transporter.
The following operon is for a sugar transporter and lacks an ABC-binding part.
(There is one, but it is for the preceding Ami gene, not the sugar gene here.)
It's sugar-binding protein has an RHS pattern,
and Pyrococcus horikoshii 2D62_A ABC-binding (that is similar in sequence to MsmK)
is on an operon near gene NP_142188 which has the RHS patterns
(just as the Ecoli RHS genes YP_026224/NP_415229/NP_418050 (rhsB/rhsC/rhsR) have these RHS patterns.
In addition, this operon contains "msm operon regulatory protein".
This operon also contains a gene to process alpha-galactosidase - is raffinose an alpha-galactosidase?
Could the nearby AmiD/AmiC oligopeptide ABC transporter be capable of translocating DLDH across the membrane?

The homologues used to build the 3D homology models for the periplasmic and membrane domains have only weak and unconvincing homology.
The resulting 3D homology models for those domains are therefore probably not good models.

This S.pneumoniae TIGR4 MglA transporter is thought to transport ribose and other sugars.

This E.coli maltose transporter that was used as a template for this S.pneumoniae 3D homology model actually does not show any significant sequence homology to the ribose transporter.
It was used as a template because this S.pneumoniae is known to be a sugar transporter and there are no 3D structures in PDB that currently have sequence homology to this S.pneumoniae transporter.

This S.pneumoniae TIGR4 MglA transporter is thought to transport ribose and other sugars.

The complex was assembled according to 2R6G (maltose ABC transporter, E.coli)

The difference between models 1, 2, and 3 for Streptococcus pneumoniae TIGR4 Rbs ribose transporter is
that different 3D structures were used to model the transmembrane subunit.
The substrate-binding and ATP-binding subunits are the same in all 3 models.

These S.pneumoniae TIGR4 sequences are the closest sequences that could be found to the E.coli Rbs ribose transporter sequences.
However, these S.pneumoniae TIGR4 sequences are probably not a ribose transporter (perhaps they are an amino acid transporter)
and S.pneumonaie probably does not actually have the Rbs ribose transporter genes.

The complex was assembled according to 2QI9 (vitamin B12 ABC transporter, E.coli)

The difference between models 1, 2, and 3 for Streptococcus pneumoniae TIGR4 Rbs ribose transporter is
that different 3D structures were used to model the transmembrane subunit.
The substrate-binding and ATP-binding subunits are the same in all 3 models.

These S.pneumoniae TIGR4 sequences are the closest sequences that could be found to the E.coli Rbs ribose transporter sequences.
However, these S.pneumoniae TIGR4 sequences are probably not a ribose transporter (perhaps they are an amino acid transporter)
and S.pneumonaie probably does not actually have the Rbs ribose transporter genes.

The complex was assembled according to 2R6G (maltose ABC transporter, E.coli)

The difference between models 1, 2, and 3 for Streptococcus pneumoniae TIGR4 Rbs ribose transporter is
that different 3D structures were used to model the transmembrane subunit.
The substrate-binding and ATP-binding subunits are the same in all 3 models.

These S.pneumoniae TIGR4 sequences are the closest sequences that could be found to the E.coli Rbs ribose transporter sequences.
However, these S.pneumoniae TIGR4 sequences are probably not a ribose transporter (perhaps they are an amino acid transporter)
and S.pneumonaie probably does not actually have the Rbs ribose transporter genes.

PDBID 2EQ7 was used as a template to make a 3D homology model of S.pneumo DLDH, using the Sali lab Modeller software.
In 2EQ7, DLDH appears as a dimer, and so the 3D homolog model is also a dimer.
RosettaDock was used to dock TIGR4_DLDH_2EQ7 to TIGR4_MsmRaf2G_2R6G.
But first, a manual dock was carried out, to dock DLDH in the general vicinity of the final destination.
The manual dock used the following clues to chose the general vicinity of the final docking destination.
Mande et al. 1996 Structure 4:277-286, PDBID 1EBD says that E2:Pro132,E2:Arg135,E2:Arg139 are conserved
and are involved in starting a binding helix (E2:Pro132) and in electrostatic binding to E3/DLDH (E2:Arg135,E2:Arg139).
Perhaps these conserved E2 residues, that bind DLDH, can be found in the sugar binding subunit of sugar transporters
that are regulated by DLDH and that perhaps also bind DLDH.
In PDBID 2EQ7 chain C, which is the E2 template used for the TIGR_DLDH_2EQ7 model,
these conserved E2 residues correspond to Pro133, Arg137, Lys142.
In TIGR4 raffinose binding protein NP_346328 that is the sequence modelled in the model TIGR4_MsmRaf2G_2R6G,
these conserved residues could correspond to Pro227, Arg230, Lys234,
which conserves a helix initiated by Pro227 which finds itself next to another helix,
with the adjacent helix ends pointing out towards the binding partner and constitute the binding interface.
PDB file of TIGR4 DLDH 3D homology model, manually oriented to bind to the TIGR4 raffinose sugar transporter TIGR4_MsmRaf2G_2R6G.PDB file of TIGR4 raffinose sugar transporter TIGR4_MsmRaf2G_2R6G, that DLDH has been docked to.